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- PDB-1wrz: Calmodulin complexed with a peptide from a human death-associated... -

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Basic information

Entry
Database: PDB / ID: 1wrz
TitleCalmodulin complexed with a peptide from a human death-associated protein kinase
Components
  • Death-associated protein kinase 2
  • calmodulin
KeywordsMETAL BINDING PROTEIN/TRANSFERASE / calmodulin / protein kinase / METAL BINDING PROTEIN-TRANSFERASE COMPLEX
Function / homology
Function and homology information


autophagosome lumen / regulation of intrinsic apoptotic signaling pathway / positive regulation of eosinophil chemotaxis / Caspase activation via Dependence Receptors in the absence of ligand / positive regulation of neutrophil chemotaxis / anoikis / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events ...autophagosome lumen / regulation of intrinsic apoptotic signaling pathway / positive regulation of eosinophil chemotaxis / Caspase activation via Dependence Receptors in the absence of ligand / positive regulation of neutrophil chemotaxis / anoikis / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / Reduction of cytosolic Ca++ levels / Activation of Ca-permeable Kainate Receptor / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / negative regulation of high voltage-gated calcium channel activity / CaMK IV-mediated phosphorylation of CREB / Glycogen breakdown (glycogenolysis) / negative regulation of calcium ion export across plasma membrane / organelle localization by membrane tethering / Activation of RAC1 downstream of NMDARs / regulation of cardiac muscle cell action potential / mitochondrion-endoplasmic reticulum membrane tethering / CLEC7A (Dectin-1) induces NFAT activation / autophagosome membrane docking / positive regulation of ryanodine-sensitive calcium-release channel activity / Negative regulation of NMDA receptor-mediated neuronal transmission / regulation of cell communication by electrical coupling involved in cardiac conduction / Unblocking of NMDA receptors, glutamate binding and activation / negative regulation of peptidyl-threonine phosphorylation / Synthesis of IP3 and IP4 in the cytosol / Phase 0 - rapid depolarisation / protein phosphatase activator activity / RHO GTPases activate PAKs / positive regulation of cyclic-nucleotide phosphodiesterase activity / positive regulation of phosphoprotein phosphatase activity / Long-term potentiation / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / catalytic complex / DARPP-32 events / detection of calcium ion / negative regulation of ryanodine-sensitive calcium-release channel activity / Smooth Muscle Contraction / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction / calcium channel inhibitor activity / cellular response to interferon-beta / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / Protein methylation / voltage-gated potassium channel complex / Activation of AMPK downstream of NMDARs / eNOS activation / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / regulation of calcium-mediated signaling / positive regulation of protein dephosphorylation / titin binding / regulation of ryanodine-sensitive calcium-release channel activity / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / Ion homeostasis / positive regulation of protein autophosphorylation / sperm midpiece / calcium channel complex / substantia nigra development / adenylate cyclase activator activity / Ras activation upon Ca2+ influx through NMDA receptor / regulation of heart rate / protein serine/threonine kinase activator activity / sarcomere / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / VEGFR2 mediated vascular permeability / positive regulation of peptidyl-threonine phosphorylation / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / VEGFR2 mediated cell proliferation / regulation of cytokinesis / regulation of autophagy / Translocation of SLC2A4 (GLUT4) to the plasma membrane / spindle microtubule / RAF activation / positive regulation of receptor signaling pathway via JAK-STAT / positive regulation of protein serine/threonine kinase activity / Transcriptional activation of mitochondrial biogenesis / Stimuli-sensing channels / spindle pole / cellular response to type II interferon / response to calcium ion / RAS processing / calcium-dependent protein binding / Inactivation, recovery and regulation of the phototransduction cascade / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / G2/M transition of mitotic cell cycle / Signaling by BRAF and RAF1 fusions / Platelet degranulation
Similarity search - Function
EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Serine/threonine-protein kinase, active site ...EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Calmodulin-1 / Death-associated protein kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKursula, P. / Vahokoski, J. / Wilmanns, M.
CitationJournal: To be Published
Title: The mode of binding of calmodulin to death-associated protein kinases
Authors: Kursula, P. / Vahokoski, J. / Wilmanns, M.
History
DepositionOct 29, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 21, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Nov 20, 2019Group: Data collection / Derived calculations
Category: diffrn_source / pdbx_struct_conn_angle / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: calmodulin
B: Death-associated protein kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3926
Polymers19,2312
Non-polymers1604
Water1,62190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-74 kcal/mol
Surface area9060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.070, 33.760, 73.870
Angle α, β, γ (deg.)90.00, 110.04, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein calmodulin /


Mass: 16852.545 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET8a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS / References: GenBank: 30584053, UniProt: P0DP23*PLUS
#2: Protein/peptide Death-associated protein kinase 2 / DAP kinase 2 / DAP- kinase related protein 1 / DRP-1


Mass: 2378.845 Da / Num. of mol.: 1 / Fragment: residues 302-320 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in Homo sapiens (human).
References: UniProt: Q9UIK4, EC: 2.7.1.37
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 37.5 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.8
Details: sodium acetate, PEG 1500, calcium chloride, pH 4.8, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8043 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 10, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8043 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 10397 / Num. obs: 10397 / % possible obs: 98 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 28 Å2 / Rsym value: 0.079 / Net I/σ(I): 11.1
Reflection shellResolution: 2→2.1 Å / Redundancy: 3 % / Mean I/σ(I) obs: 3.5 / Num. unique all: 1421 / Rsym value: 0.364 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.2.0000refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.87 / SU B: 13.594 / SU ML: 0.2 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: TLS REFINEMENT / Cross valid method: THROUGHOUT / σ(F): -3 / ESU R: 0.277 / ESU R Free: 0.219 / Stereochemistry target values: Engh & Huber
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS DURING REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.27872 520 5 %RANDOM
Rwork0.22441 ---
all0.22711 10396 --
obs0.22711 10396 98.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 36.022 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å20 Å20.37 Å2
2--0.08 Å20 Å2
3----0.41 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1328 0 4 90 1422
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0211392
X-RAY DIFFRACTIONr_bond_other_d0.0020.021228
X-RAY DIFFRACTIONr_angle_refined_deg0.9881.9561867
X-RAY DIFFRACTIONr_angle_other_deg0.77332872
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5795174
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.80425.32577
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.98815266
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.531511
X-RAY DIFFRACTIONr_chiral_restr0.0590.2202
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021592
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02278
X-RAY DIFFRACTIONr_nbd_refined0.1940.2446
X-RAY DIFFRACTIONr_nbd_other0.2020.21550
X-RAY DIFFRACTIONr_nbtor_other0.0840.2831
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.264
X-RAY DIFFRACTIONr_metal_ion_refined0.1480.215
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1810.223
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1950.273
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2220.213
X-RAY DIFFRACTIONr_mcbond_it0.6822898
X-RAY DIFFRACTIONr_mcbond_other0.1112355
X-RAY DIFFRACTIONr_mcangle_it1.0531372
X-RAY DIFFRACTIONr_scbond_it1.1214568
X-RAY DIFFRACTIONr_scangle_it1.4665495
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.307 39
Rwork0.275 743
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.4776-3.5799-3.943912.65092.660720.1772-0.128-0.237-0.0509-0.32580.0702-0.24360.6635-0.00620.05780.24820.0416-0.051-0.02520.0074-0.219315.5656-0.02739.1508
27.4375-2.5041-0.33172.5046-0.36553.71820.10410.4184-0.2425-0.1133-0.08850.18080.20380.0178-0.0156-0.2450.0308-0.0016-0.2278-0.0227-0.156612.250511.648427.4472
316.2638-8.4429-12.070214.58674.570622.9594-0.5607-0.6563-0.55140.06890.56670.00691.49411.2367-0.0060.04960.0756-0.0444-0.0497-0.0308-0.181813.32573.456619.6406
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA81 - 14882 - 149
2X-RAY DIFFRACTION1AE - F153 - 1541
3X-RAY DIFFRACTION2AA2 - 803 - 81
4X-RAY DIFFRACTION2AC - D151 - 1521
5X-RAY DIFFRACTION3BB302 - 3201 - 19

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